Release v0.5.0

Resource label and value adjustments along with some code cleanup

Parameter Changes

• Max resource parameters added

General Developer Changes

• Switched to the nf-core resource labels
  • Adjusted default resource values
  • Added in the time directive
  • Added in the max_ params

Release v0.4.0

Adding in downsampling options along with some code clean-up and environment adjustments

Additions

• The following parameters pertaining to downsampling have been added:
  • --downsample - Turns on downsampling with seqtk
  • --downsample_count - Approximate number of reads to be kept
  • --downsample_seed - The random seed to use for downsampling
  • --downsample_amplicons - Downsample with regards to keeping amplicons at approximately the same coverage threshold using samtools

Parameter Changes

• New profile - mamba
  • Separates out conda and mamba for more user control

Output Changes

• The summary CSV file (removal_summary.csv) has additional columns added when running with downsampling

General Developer Changes

• Nextflow code restructuring
  • Duplicate modules removed
  • Updated outputs to use path over file
• Python code restructuring to follow better practices in documenting functions
• Adjusted how the versions output is created

Release v0.3.0

General Developer Changes

• Adjusted how conda is implemented to support new releases of Nextflow
• Fixed integration tests

Release v0.2.0

Argument Changes:

• Added --keep_ref_id <ID> as an argument for illumina and nanopore fastq data
  • Allows for a different reference ID to be kept if the reference sequence is changed
• Removed --covid_ref_id <ID> as an illumina specific argument
  • Replaced by above
• Removed the illumina_threads and nanopore_threads resource arguments that were not super useful
  • Changed to using task.cpus to keep everything in line
  • Resources should be changed using the process name or the process tag now

Parameter Changes:

• Default minimum read length for nanopore data (--min_length) set to 350 from 400 to better accommodate shorter amplicon schemes
• Help command updated

Output Changes:

• New output file: process_versions.yml
  • File contains the process name along with which tools and their versions was used in it

General Developer Changes:

• Changed code order for nanopore workflows
  • All minimap2 code should be above nanostripper in the files now
• General reformatting of code to try to make everything more consistent/cohesive

Initial Release v0.1.0

Initial release, pipeline seems to be in a good spot at the moment